README.md

LIGER (Linked Inference of Genomic Experimental Relationships)

LIGER (liger) is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.

LIGER can be used to compare and contrast experimental datasets in a variety of contexts, for instance:

Additional Installation Steps for MacOS (recommended before step 4)

Installing RcppArmadillo on R>=3.4 requires Clang >= 4 and gfortran-6.1. Follow the instructions below if you have R version 3.4.0-3.4.4. These instructions (using clang4) may also be sufficient for R>=3.5 but for newer versions of R, it's recommended to follow the instructions in this post.

Uncompress the resulting zip file and type into Terminal (sudo if needed):

mv /path/to/clang4/ /usr/local/

Create .R/Makevars file containing following:

# The following statements are required to use the clang4 binary
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
CXX11=/usr/local/clang4/bin/clang++
CXX14=/usr/local/clang4/bin/clang++
CXX17=/usr/local/clang4/bin/clang++
CXX1X=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib

For example, use the following Terminal commands:

cd ~
mkdir .R
cd .R
nano Makevars

Paste in the required text above and save with Ctrl-X.

Detailed Instructions for FIt-SNE Installation for use in runTSNE (recommended for large datasets)

Using FIt-SNE is recommended for computational efficiency when using runTSNE on very large datasets.
Installing and compiling the necessary software requires the use of git, FIt-SNE, and FFTW. For a
basic overview of installation, visit this page.

Basic installation for most Unix machines can be achieved with the following commands after downloading
the latest version of FFTW from here. In the fftw directory, run: